Install Python module for Blender
You need modules that work with the same Python version as the one shipped with blender (currently, blender 2.78 is shipped with Python 3.6.0).

My favorite Python distribution is anaconda. Here are the steps I just followed for blender 2.78 in linux (a similar setup should be easy to get for windows or macos).


Install anaconda.
Create an specific environment for the modules you need in blender: 




conda create --name conda-python-blender python=3.6.0



Activate this environment:




source activate conda-python-blender



Install all your required libraries ("modules"):




conda install cython



You can also use pip if your library is not (yet) in anaconda repositories:




pip install mdtraj



Figure out the directory where your libraries are stored:




echo "import sys; print(sys.path)" | python


In my case, I get:



['', '/home/christophe/anaconda3/envs/conda-python-blender/lib/python36.zip', '/home/christophe/anaconda3/envs/conda-python-blender/lib/python3.6', '/home/christophe/anaconda3/envs/conda-python-blender/lib/python3.6/lib-dynload', '/home/christophe/anaconda3/envs/conda-python-blender/lib/python3.6/site-packages', '/home/christophe/anaconda3/envs/conda-python-blender/lib/python3.6/site-packages/setuptools-27.2.0-py3.6.egg']


You want the "site-packages" directory, so, in my case:



/home/christophe/anaconda3/envs/conda-python-blender/lib/python3.6/site-packages





Open blender, then go to the Python console and do the following as Rich Colburn said, that is adding the previous directory the the path where Python is looking for libraries:




  import sys
  sys.path.append('/home/christophe/anaconda3/envs/conda-python-blender/lib/python3.6/site-packages')




And that's it!


Optional step. If you want to make it permanent so that every time you open a new blender file, blender adds automatically the required directory to the path, then save the following lines in a file (say add-anaconda-libs-to-path.py) and put the file in ./scripts/startup/ (for me it is /home/christophe/.config/blender/2.78/scripts/startup/.




import sys
sys.path.append('/home/christophe/anaconda3/envs/conda-python-blender/lib/python3.6/site-packages')
def register():
    print("Added anaconda library to path")


A final note: unless you want to update your libraries with conda, you don't have to activate the conda-python-blender environment anymore as blender will use its own Python interpreter.